You can access Thomas Jefferson’s book, Notes on the State of Virginia, here. In discussing rights and God, my co-blogger at American Creation Tom Van Dyke has repeatedly mentioned on these comment threads one of Jefferson’s passages from that book which you can read in context here. The following is the relevant passage from Jefferson’s book:

And can the liberties of a nation be thought secure when we have removed their only firm basis, a conviction in the minds of the people that these liberties are of the gift of God? That they are not to be violated but with his wrath? Indeed I tremble for my country when I reflect that God is just: that his justice cannot sleep for ever: that considering numbers, nature and natural means only, a revolution of the wheel of fortune, an exchange of situation, is among possible events: that it may become probable by supernatural interference! The Almighty has no attribute which can take side with us in such a contest.

Jefferson is discussing slavery and mentions we are bound to see God’s wrath for violating the natural rights of blacks. Jefferson also, interestingly, makes racist observations about his black slaves, which I will not reproduce here (you can read them in the original). Yet, both of those sentiments (about God given rights, but also, racist observations) did not (as far as I know) raise controversy in the Founding era like they might today.

But our rulers can have authority over such natural rights only as we have submitted to them. The rights of conscience we never submitted, we could not submit. We are answerable for them to our God. The legitimate powers of government extend to such acts only as are injurious to others. But it does me no injury for my neighbour to say there are twenty gods, or no god. It neither picks my pocket nor breaks my leg.

I should note that all of the key Founders — Washington, J. Adams, Jefferson, Madison, Franklin, G. Morris, Hamilton, Wilson, etc. — believed in free exercise of religion or an “unalienable right to conscience,” universally applicable to atheists, polytheistics, heretics and infidels of every denomination. They DIFFERED on proper establishment policy. Those who saw a greater role for government & religion acting together (mild religious establishments) like J. Adams and Washington were better able to placate the forces of religious correctness who reacted to Jefferson’s above quoted sentiment with the following. From John Mitchell Mason:

“It does me no injury; it neither picks my pocket, nor breaks my leg.” This is perfectly of a piece with his favorite wish to see a government administered without any religious principle among either rulers or ruled. Pardon me, Christian: this is the morality of devils, which would break in an instant every link in the chain of human friendship, and transform the globe into one equal scene of desolation and horror, where fiend would prowl with fiend for plunder and blood–yet atheism “neither picks my pocket nor breaks my leg.” I will not abuse you by asking, whether the author of such an opinion can be a Christian? or whether he has any regard for the scriptures which confines all wisdom and blessedness and glory, both personal and social, to the fear and the favor of God?

Jefferson’s election and subsequent reelection illustrates how the forces of religious correctness — the orthodox Trinitarian Christians, many of them Calvinists, who wished to see society ruled by their religion — lost much ground during the American Founding. I think they mistakenly thought men like J. Adams and Washington were reliable allies. They supported the conservative Christians’ right to freely exercise their religion and valued how their Christianity helped make men moral, and hence self governable. However, neither wanted society to be ruled by such “biblical Christians” — the religious right of the Founding era. As noted above, all key Founders believed in granting religious rights to non-Christians, which itself is tantamount to giving non-believers a natural right to sin. Refusing to worship the orthodox Christian God and worshipping and proselytizing for false gods are grave sins according to orthodox biblical Christianity. And this necessarily results when you grant free exercise rights to non-orthodox Christians. This is why Calvin helped see Servetus burned at the stake in Geneva for openly promoting denial of the Trinity.

Yet, it should be noted that there were evangelicals of the Founding era, the Baptists like John Leland, operating in the tradition of Roger Williams who didn’t believe the state should enforce orthodox religious conscience. That is the kind of orthodox Christianity that is more compatible with American Founding ideals. In fact, they were Jefferson’s and Madison’s key allies in defeating the forces of “religious correctness” and delivering America a constitutional republic that values religious and political liberty.